Gene-set Collections

16-12-2010 Release GO-Pathways-PFAM

Sources

Gene-Ontology BP, CC, MF (up-propagated, all evidence codes)
KEGG Pathways
NCI Pathways
Biocarta Pathways
PFAM Protein Domains

R Code and Release Notes

R code to format the gene-sets

R Code

Gene-sets (GMT format)

GMT is the standard gene-set format adopted by a few resources, such as GSEA. Original description page

RELEASE INFO

org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db 
(GO, KEGG gene-set ID to gene ID)
- Package version: 2.4.6 
- R version: 2.12.0
- Packaged: 2010-10-04
- Built: 2010-10-21

GO.db
(GO gene-set ID to name)
- Package version: 2.4.5
- R version: 2.12.0
- Packaged: 2010-09-23
- Built: 2010-10-21

KEGG.db
(KEGG pathway ID to name)
- Package version: 2.4.5
- R version: 2.12.0
- Packaged: 2010-09-23
- Built: 2010-10-21

NCI 
- annotations downloaded from website (Uniprot ID, human): 2010-11-08

BioCarta
- annotations downloaded from WhichGenes (Entrez-Gene ID, human): 2010-03-26

PFAM
...

Orthology Table

NCBI Homologene Build 65

Questions?

email: daniele [dot] merico [atsign] gmail [dot] com